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source("tianfengRwrappers.R")

载入需要的程辑包：reticulate
载入需要的程辑包：tidyr

载入程辑包：‘MySeuratWrappers’

The following objects are masked from ‘package:Seurat’:

    DimPlot, DoHeatmap, LabelClusters, RidgePlot, VlnPlot


载入程辑包：‘ggpubr’

The following object is masked from ‘package:rbokeh’:

    set_palette


载入程辑包：‘cowplot’

The following object is masked from ‘package:ggpubr’:

    get_legend

载入需要的程辑包：viridisLite

载入程辑包：‘reshape2’

The following object is masked from ‘package:tidyr’:

    smiths

NOTE: Either Arial Narrow or Roboto Condensed fonts are required to use these themes.
      Please use hrbrthemes::import_roboto_condensed() to install Roboto Condensed and
      if Arial Narrow is not on your system, please see https://bit.ly/arialnarrow
clusterProfiler v3.14.3  For help: https://guangchuangyu.github.io/software/clusterProfiler

If you use clusterProfiler in published research, please cite:
Guangchuang Yu, Li-Gen Wang, Yanyan Han, Qing-Yu He. clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS: A Journal of Integrative Biology. 2012, 16(5):284-287.
Registering fonts with R

载入程辑包：‘plotly’

The following object is masked from ‘package:ggplot2’:

    last_plot

The following object is masked from ‘package:stats’:

    filter

The following object is masked from ‘package:graphics’:

    layout

载入需要的程辑包：e1071
Registered S3 methods overwritten by 'proxy':
  method               from    
  print.registry_field registry
  print.registry_entry registry

载入程辑包：‘widgetTools’

The following object is masked from ‘package:dplyr’:

    funs


载入程辑包：‘DynDoc’

The following object is masked from ‘package:BiocGenerics’:

    path


载入程辑包：‘IDPmisc’

The following object is masked from ‘package:shiny’:

    hr


载入程辑包：‘DT’

The following objects are masked from ‘package:shiny’:

    dataTableOutput, renderDataTable

The following object is masked from ‘package:Seurat’:

    JS

========================================
circlize version 0.4.13
CRAN page: https://cran.r-project.org/package=circlize
Github page: https://github.com/jokergoo/circlize
Documentation: https://jokergoo.github.io/circlize_book/book/

If you use it in published research, please cite:
Gu, Z. circlize implements and enhances circular visualization
  in R. Bioinformatics 2014.

This message can be suppressed by:
  suppressPackageStartupMessages(library(circlize))
========================================

载入需要的程辑包：grid
========================================
ComplexHeatmap version 2.2.0
Bioconductor page: http://bioconductor.org/packages/ComplexHeatmap/
Github page: https://github.com/jokergoo/ComplexHeatmap
Documentation: http://jokergoo.github.io/ComplexHeatmap-reference

If you use it in published research, please cite:
Gu, Z. Complex heatmaps reveal patterns and correlations in multidimensional 
  genomic data. Bioinformatics 2016.
========================================


载入程辑包：‘ComplexHeatmap’

The following object is masked from ‘package:plotly’:

    add_heatmap

功能分析

BMP相关基因

BMP通路相关

gsave("BMPreceptor_ds1.png", device = png, plot = Dotplot(c("BMPR1A","BMPR1B"),ds1), height = 6, width = 5)

Error in gsave("BMPreceptor_ds1.png", device = png, plot = Dotplot(c("BMPR1A",  : 
  没有"gsave"这个函数

雷达图 fig4

library(fmsb)
data <- read.csv("./go_res.csv",row.names = 1,quote = "", check.names=FALSE)
# data=as.data.frame(matrix(sample(0:50, 18,replace=T) , ncol=6))
# colnames(data)=c('IL-1 signaling pathway','Response to IFNa','NFkB signaling pathway','IL-6 signaling pathway', 'Muscle contraction','Response to IFNr')
# rownames(data) <- c('Monocyte','Neutrophil','Macrophage')
# 用于生成雷达图的最大最小值
data=rbind(rep(15,5) , rep(-10,5) , data)


colors_border <- colors_list[c(4,1,5)]
colors_in <- aero_colors_list[c(4,1,5)]

svg("GO_res.svg",height = 8,width = 10)
radarchart(data, axistype=0, seg = 5,
 pcol=colors_border, pfcol=colors_in, plwd=1.3 , plty=1,pty=32,
 cglcol="black", cglty=3, cglwd=0.6,
)
legend(x=-1.6, y=0.5, legend = rownames(data[-c(1,2),]), bty = "n", pch=20 , col=colors_border, text.col = "black", cex=1, pt.cex=2)
dev.off()

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